"They went to Capernaum, and when the Sabbath came, Jesus went into the synagogue and began to teach."(Mark 1:21)

The ruins of a great synagogue were first identified in 1866 during a survey by the British cartographer Captain Charles W. Wilson. Partially reconstructed in 1926, the dating of the Capernaum synagogue continues to be a matter of debate. What is certain is that the imposing ruin is not the synagogue referred to in the Gospel of Mark, though it seems to have been built on the site of an earlier 1st-century building.

Built of imported white limestone on basalt stone foundations, the floor plan is similar to the 4th-century synagogue at Chorazim (Korazim, 4 km to the north), and the 3rd-century synagogue at Baram (in the northern Galilee), but the architectural ornamentation of the Capernaum building is far more elaborate, with Corinthian capitals and intricately carved stonework reliefs (vine and fig leaves, geometric designs, eagles, etc.). One relief carving of a cart may depict a portable Ark of the Covenant. Visitors are sometimes disconcerted by the fact that the architectural decoration also includes swastikas; but this was a common geometrical design of the period.

A 4th-century Aramaic inscription on one of the broken columns records the name of the donor, "Halfu, son of Zebida". These names in the Greek form (Alphaeus and Zebedee) are mentioned in the New Testament.

The synagogue as it appeared in 381 was described by the Spanish pilgrim, the Lady Egeria, who reported that the way into the structure was up many steps, and that the building was made of dressed stone.

The very grandeur of the Capernaum synagogue has contributed to the controversy concerning the actual dating of the building. Various theories have been proposed. Evidence for a 4th-century date is based in part on coins and pottery found beneath the floor. Proponents of an earlier 2nd-century date say these may have been left during later repairs and reconstruction, possibly following the earthquake of 363. Another possibility is that the synagogue was built during the short reign (361-363) of the Emperor Julian "the Apostate", which would also correspond with the date of the earthquake.

The synagogue and the church at Capernaum were both destroyed in the early 7th century (sometime before the Arab conquest in 636). In light of the continuing tensions between the Christian and Jewish communities, it has been suggested that the church may have been destroyed during the Persian invasion of 614, and that the synagogue was destroyed 15 years later as an act of retaliation during the brief re-establishment of Byzantine rule. If so, it is appropriate that one of the first instances of modern "inter-faith dialogue" between Christians and Jews took place in nearby Tiberias in 1942, in a series of discussions between the Rev. George L. B. Sloan, a minister of the Church of Scotland in Tiberias, and the Jewish writer and lecturer Dr. Shalom Ben-Chorin.